Global warming due to exhaust emissions, rapid depletion of crude oil, and strict carbon control legislation has forced researchers to search biofuels as substitute for petroleum diesel fuels. Biodiesel is a renewable and oxygenated fuel. It is free from sulfur, non-toxic and a biodegradable. The different non-edible vegetable oils such as Algae, Karanja and Jatropha could be used to produce biodiesel. Biodiesel is a green fuel with an exception that it emits 15-20% more NOx as compared to diesel fuel. The emissions of nanoparticles are more hazardous to human health. The nanoparticles emission of biodiesel must be measured according to the new strict regulations. The engine performance and the lower emission characteristics, except for NOx emission, for Algae, Karanja and Jatropha oil biodiesels are similar to those of diesel fuel. Present study has investigated the performance, combustion and emissions, including nanoparticle emissions, for Algae, Karanja and Jatropha oil biodiesel using CeO2 as fuel additive in military heavy duty, 582kW, CIDI engine. In research investigations, engine power output with Algae, Karanja, and Jatropha biodiesel fuel was found to be marginally lower as compared to diesel fuel. Biodiesel fuels blended with Cerium oxide as fuel additive, resulted in lower engine exhaust emissions with 22-28% reduction in NOx emissions as well as lower nanoparticle emissions.